[BioC] GenomeGraphs issue

[Zoppoli, Gabriele (NIH/NCI) [G]]

Hi everybody,

I'm trying to plot the exon probeset values for a gene, but alternative transcripts from Ensembl, or what GenomeGraphs calls "AffyModel" in the legend do not show up. Everything is the same as in the GenomeGraphs manual (and this is the problem!). Here is everything, including the txt files I used:

require(GenomeGraphs)

title <- makeTitle(text = "ENSG00000172716", color = "darkred")

exon <- makeExonArray(intensity = undata, probeStart = unposition[, 3], probeEnd = unposition[,4], probeId = as.character(unposition[,1]),
nProbes = unprobes, dp = DisplayPars(color = "blue", mapColor = "dodgerblue2"), displayProbesets = FALSE)

affyModel.model <- makeGeneModel(start = unposition[,3], end = unposition[, 4])
# note that if you use this in the gdplot function, you will have a green gene, whereas with affyModel you get a blue gene

affyModel <- makeAnnotationTrack(start = unposition[,3], end = unposition[, 4], feature = "gene_model",
group = "ENSG00000172716", dp = DisplayPars(gene_model = "darkblue"))
#adding this in gdplot returns a blue gene

gene <- makeGene(id = "ENSG00000172716", biomart = mart)
#no sign of this even after calling it in gdplot, and the legend shows that something yellow should appear

transcript <- makeTranscript(id = "ENSG00000172716", type = "ensembl_gene_id", biomart = mart)
#I suppose from other examples in GenomeGraphs that this should show the splice variants in Ensembl below the Affy model, but nothing appears

legend <- makeLegend(c("affyModel", "gene"), fill = c("darkgreen", "orange"))

rOverlay <- makeRectangleOverlay(start = 30701442,
end = 30724798, region = c(3, 5),
dp = DisplayPars(alpha = 0.2, fill = "olivedrab1"))

gdPlot(list(title, exon, affyModel, gene, transcript, legend), minBase = 30701442,
maxBase = 30724798,overlay = rOverlay)
#note that since I don't want to overlay anything, I just used it as a box to encase the whole gene


> sessionInfo()
R version 2.10.1 (2009-12-14) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GenomeGraphs_1.6.0     biomaRt_2.2.0          aroma.affymetrix_1.5.0 aroma.apd_0.1.7       
 [5] affxparser_1.18.0      R.huge_0.2.0           aroma.core_1.5.0       aroma.light_1.16.0    
 [9] matrixStats_0.2.1      R.rsp_0.3.6            R.cache_0.3.0          R.filesets_0.8.1      
[13] digest_0.4.2           R.utils_1.4.0          R.oo_1.7.2             R.methodsS3_1.2.0     

loaded via a namespace (and not attached):
[1] RCurl_1.3-1  tools_2.10.1 XML_2.8-1   

Thank you all!

Gabriele Zoppoli, MD
Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy
Guest Researcher, LMP, NCI, NIH, Bethesda MD

Work: 301-451-8575
Mobile: 301-204-5642
Email: zoppolig at mail.nih.gov
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: undata.txt
URL: <https://stat.ethz.ch/pipermail/bioconductor/attachments/20100515/dea170dd/attachment.txt>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: unposition.txt
URL: <https://stat.ethz.ch/pipermail/bioconductor/attachments/20100515/dea170dd/attachment-0001.txt>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: unprobes.txt
URL: <https://stat.ethz.ch/pipermail/bioconductor/attachments/20100515/dea170dd/attachment-0002.txt>